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I feel like there are other words that do this "inexplicably voicing the first mora" thing too (though I can't think of any examples off the top of my head), so maybe those could offer some insight into #2.
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rintaunNov 28 '12 at 18:49

1 Answer
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The readings サ・シャ are from the Chinese morpheme shā. Usually, when 砂 is read サ or シャ, it represents the Japanese version of this morpheme.

In this case, 砂 represents ザ・ジャ, which has a similar sound and meaning. Since the reading isn't quite the same, it's a hint that it might not represent the same morpheme. I decided to search for support for this idea by looking into the etymology of じゃり. Although I don't have access to 日本国語大辞典 myself, I found a blogger who researched the subject and posted about it:

This seemed to confirm the idea. It appears that じゃり was originally of Japanese origin, and was spelled with the kanji 砂利 at a later date. Presumably they were chosen because 砂 represented a similar meaning, while 砂 and 利 together represented a similar sound. Because of this, the reading became an exception.

As for your other question, it appears that both じゃり and ざり used to be common, but じゃり is more common in modern Japanese. Perhaps someone else will be able to be more specific on this point.

(I'm a bit outside my comfort zone on this post, so if anyone has corrections or confirmation to give, I would be most grateful.)

This answer needs revision--I appear to have mixed up my sources, and the link here doesn't seem to say what this answer suggests. I read somewhere about a historical interplay between さ and しゃ, though. I should come back to this answer and fix it after doing more research…
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snailboat♦Jun 20 '14 at 10:36